Mercurial > repos > cpt > cpt_psm_recombine

annotate PSM_Recombine.xml @ 1:97ef96676b48 draft

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author cpt
date Mon, 05 Jun 2023 02:51:26 +0000
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children d09346afadfa
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1 <tool id="edu.tamu.cpt.external.psm_recombine" name="PSM Prep and Table Generator:" version="21.0.0">
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2 <description>: generates a raw PSM file for plotting and a tabular summary</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>cpt-macros.xml</import>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="5.22.1">perl</requirement>
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9 <requirement type="package">perl-bioperl</requirement>
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10 <requirement type="package">perl-moose</requirement>
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11 <requirement type="package">perl-ipc-run</requirement>
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12 <requirement type="package">perl-getopt-long-descriptive</requirement>
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13 <requirement type="package" version="3.7">python</requirement>
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14 <requirement type="package" version="1.74">biopython</requirement>
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15 </requirements>
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16 <command detect_errors="aggressive"><![CDATA[
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17 perl -Mlib='$__tool_directory__/lib' '$__tool_directory__/cpt_psm_0_prep.pl'
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18 --galaxy
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19 --outfile_supporting '$__new_file_path__'
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20 #for $item in $repeat_file:
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21 --file "${item.file}"
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22 #end for
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23
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24 --cpt_psm_object "${cpt_psm_object}"
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25
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26 --cpt_psm_object_files_path "${cpt_psm_object.files_path}"
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27
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28 --cpt_psm_object_format "TXT"
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29
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30 --cpt_psm_object_id "${cpt_psm_object.id}"
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31
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32 &&
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33
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34 mkdir tmp_001
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35 &&
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36 mkdir tmp_002
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37
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38 &&
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39
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40 perl -Mlib='$__tool_directory__/lib' '$__tool_directory__/cpt_psm_2_gentable.pl'
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41 --galaxy
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42 --outfile_supporting '$__new_file_path__'
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43 --file "${cpt_psm_object}"
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44
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45 #if $evalue and $evalue is not "None":
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46 --evalue "${evalue}"
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47 #end if
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48
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49 #if $dice and $dice is not "None":
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50 --dice "${dice}"
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51 #end if
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52
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53 #if $mismatch and $mismatch is not "None":
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54 --mismatch "${mismatch}"
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55 #end if
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56
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57 #if $gap_penalty and $gap_penalty is not "None":
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58 --gap_penalty "${gap_penalty}"
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59 #end if
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60
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61 #if $match and $match is not "None":
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62 --match "${match}"
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63 #end if
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64
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65 --diff_table "./tmpDiff.tsv"
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66 --diff_table_files_path "./tmp_001"
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67 --diff_table_format TSV_U
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68 --diff_table_id "000001"
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69
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70 --blastclust "./tmpClust.tsv"
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71 --blastclust_files_path "./tmp_002"
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72 --blastclust_format TSV_U
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73 --blastclust_id "000002"
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74
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75 &&
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76
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77 '$__tool_directory__/PSM_Recombine.py'
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78 ./tmpDiff.tsv
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79 #for $item in $repeat_file:
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80 "${item.file}"
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81 #end for
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82 > "${tableOut}"
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83 ]]>
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84 </command>
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85 <inputs>
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86 <repeat name="repeat_file" title="Genbank file(s) used to generate PSM">
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87 <param name="file" optional="False" label="Gbk file" type="data" format="genbank"/>
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88 </repeat>
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89 <param value="0.0001" name="evalue" help="Evalue cutoff" optional="True" label="evalue" type="float"/>
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90 <param value="50" name="dice" help="Dice cutoff" optional="True" label="dice" type="float"/>
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91 <param value="-1" name="mismatch" help="Mismatch Score" optional="True" label="mismatch" type="float"/>
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92 <param value="0.0" name="gap_penalty" help="Gap Penalty" optional="True" label="gap_penalty" type="float"/>
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93 <param value="5" name="match" help="Match Score" optional="True" label="match" type="float"/>
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94 </inputs>
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95 <outputs>
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96 <data format="tabular" name="tableOut" label="PSM Tabular Results"/>
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97 <data name="cpt_psm_object" label="Raw PSM Binary output" format="TXT"/>
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98 </outputs>
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99 <help><![CDATA[
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100 **What it does**
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101
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102 This tool takes in 2 or more GenBank files, blasts, and prepares data
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103 structures for use in the companion tool, PSM Plotter, as well as a
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104 tabular file read-out of the results. Select as many (multi)-gbk files
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105 as you *might* want to plot. Once this tool is done, you can select
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106 any subset of those to plot then.
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107
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108 IMPORTANT PARAMETERS
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109 --------------------
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110
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111 - ``mismatch``, ``gap_penalty``, ``match``
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112
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113 These parameters control the Needleman-Wunsch Multiple Sequence
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114 Alignment library's scoring scheme. Mismatch scores are generally
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115 negative and discourage unrelated proteins from being plotted in a
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116 line together. Match scores encourage related proteins to line up.
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117 Gap penalty is set at zero as we generally prefer gaps to mismatches
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118 in this tool; phage genomes are small and gaps are "cheap" to use,
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119 whereas mismatches can sometimes give an incorrect impression of
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120 relatedness. That said, how your plots look is completely up to you
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121 and we encourage experimentation!
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122 ]]></help>
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123 <expand macro="citations-2020"/>
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124 </tool>